rs6889356

Variant names:

• chr5-147894213-T-C
• rs6889356
• NM_206966.3:c.*10-1274A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206966.3(C5orf46):​c.*10-1274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,138 control chromosomes in the GnomAD database, including 4,747 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (4747 hom., cov: 31)
• Consequence: C5orf46 NM_206966.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 1 publications found

Genes affected

C5orf46 (HGNC:33768): (chromosome 5 open reading frame 46) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206966.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf46	NM_206966.3	MANE Select	c.*10-1274A>G		intron	N/A	NP_996849.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf46	ENST00000318315.5	TSL:1 MANE Select	c.*10-1274A>G		intron	N/A	ENSP00000315370.4
	C5orf46	ENST00000955897.1		c.*9+2771A>G		intron	N/A	ENSP00000625956.1
	C5orf46	ENST00000955898.1		c.*9+2771A>G		intron	N/A	ENSP00000625957.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22894 AN: 152020 Hom.: 4718 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.00963

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.00762

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152138 Hom.: 4747 Cov.: 31 AF XY: 0.147 AC XY: 10973 AN XY: 74398

African (AFR) AF: 0.475 AC: 19659 AN: 41420

American (AMR) AF: 0.0652 AC: 996 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3468

East Asian (EAS) AF: 0.00965 AC: 50 AN: 5180

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4832

European-Finnish (FIN) AF: 0.00762 AC: 81 AN: 10626

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0237 AC: 1613 AN: 68010

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.0550 Hom.: 1078

Bravo AF: 0.169

Asia WGS AF: 0.0470 AC: 165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6889356; hg19: chr5-147273776;